Sephiroth, his own man or a puppet?

That explanation doesn't make a ton of sense to me. He had no emotional connection to Jenova. He had no real ties to her at all, therefore, why would it anger him to learn that Shinra experimented on a deranged space monster?

My interpretation is that had Jenova truly been dead, he probably would have been pissed off about being lied to, but he wouldn't have become a deranged murderer. She manipulated and amplified his decision-making abilities, thereby guiding his actions in a very subtle and very general manner.

There was no way for her to manipulate his emotions unless he had certain emotions to manipulate. Hence the reason Sephiroth didn't freak out until after he learned the truth. Once he learned about Jenova, she used his birthing outrage and amplified it, manipulating these specific emotions that he never had before because he didn't know the truth.

There's no real way to determine the absolute truth, in any case. These topics were left to be ambiguous so that people would discuss them and discover their own version of the truth. Frankly, I don't find it terribly interesting (or logical) to think that Sephiroth became a psychotic killer with delusions of grandeur because he read a few top secret files. I find it a lot more complex and interesting to think that Sephiroth's rise to evil was a combined effort between his fragile subconscious and Jenova's manipulations.

On top of that, if Sephiroth was entirely responsible for his own violent changes, that would make Jenova a pretty pointless character in the game. If that's the case, then all she really is is a weird looking boss with some background plot attached to her. I find it more interesting to think that she had a more active role in his villainous deeds.